What are "Mutations"?

It is a semantics game. In many senses they are correct but you all are using the terms differently. He identifies patterns in mutations that skew towards helpfulness and declares them non random, that’s it. A great example is immune system. Mutations are directed to hyper variable region, therefore not random with respect to fitness.

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Shapiro has published 3 papers on the subject in addition to his book.
I will link to one which is freely available.

He summarises how he views evolution happens as below:

Blockquote
Although there remain many gaps in our knowledge, we are now in a position to outline a distinctively 21st century scenario for evolutionary change. The scenario includes the following elements:

(1) hereditary variation arises from the non-random action of built-in biochemical systems that mobilize DNA and carry out natural genetic engineering;

(2) major disruptions of an organism’s ecology trigger cell and genome restructuring. The ecological disruptions can act directly, through stress on individuals, or indirectly, through changes in the biota that favour unusual interactions between individuals (cell fusions, interspecific hybridizations). Triggering events continue until a new ecology has emerged that is filled with organisms capable of utilizing the available resources;

(3) ecologically-triggered cell and genome restructurings produce organisms which, at some frequency, will possess novel adaptive features that suit the altered environment. Novel adaptive features can be complex from the beginning because they result from processes that operate on pre-existing functional systems, whose components can be amplified and rearranged in new combinations. Competition for resources (purifying selection) serves to eliminate those novel system architectures that are not functional in the new ecology;

(4) once ecological stability has been achieved, natural genetic engineering functions are silenced, the tempo of innovation abates, and microevolution can occur to fine-tune recent evolutionary inventions through successions of minor changes.

You will need to read the paper to understand where he is coming from. He has referenced 209 papers to support his claims. I have only read the paper. Haven’t looked up any of his references.

And this is a classic example of why I object to EES too. Not because the science is wrong, but because is merely a rewording of well know science, and abuse of much terminology (like random).

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I think it’s more of a difference in emphasis. Leading to a difference in opinion as to what is the norm.
For example, if you listen to Lynn Margulies, most speciation happens through symbiosis. Obviously other biologists will disagree, even as they acknowledge symbiosis happens.
It seems to me that biologists who work with plants, microbes, bacteria etc view evolution differently from those who work with mammals. Or atleast some of them (who happen to be more famous) do.

Perhaps you need to stand in their shoes and look at what they are looking at day in and day out… and vice versa.
I don’t think its just semantics.

Not in his use of the word “random”. That usuage is unjustifiable without total ingorance or denial of probability theory and statistics.

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Evolutionists I have discussed this with hate the “random” word more then the creationists do. They insist that natural selection is not a random process. They realize random change through a sequence has a low probability of finding anything.

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Natural selection is not random, but the environmental changes are unpredictable, and therefore random in an important sense. Mutations are random, but also have patterns within them, and identifying and understanding these patterns is a fundamental engine for the progress of biology. Do you see the duality?

I think so.

I pretty much agree here with the uncertainty if this process will create a pattern over time that is mostly random. It is not clear to me how sequence change gets translated to fitness other the purifying selection in some cases reducing fitness loss in a population.

This is a very good point you are making.

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That is exactly my position as well. EES is much more about salesmanship than the actual science. The way in which Shapiro plays around with the word “random” is a perfect example.

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Symbiosis simply defines the selective pressures that act on random mutations. What Margulis proposes is completely within the standard theory of evolution.

What I was hoping for was focusing on one of those 209 references and seeing how it supports Shapiro’s claims.

Natural selection isn’t a random process which is probably why scientists react when it is described as random.

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I think of the scale of random vs high correlation it is much closer to random over time as it is hard to correlate DNA change to positive selection.

Not quite. She thought symbiosis was the major process driver in evolution: New species and traits emerge through the symbiotic relationship between two or more kinds of organisms. While it’s true that new species can emerge through such a route, it’s a stretch to suggest that most do. That, and a lot of hand-waving about poorly specified mechanisms on her part. She never really filled in the details. I think Margulis only had one tool in her toolbox: call it a hammer. She treated every question like a nail.

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Unless there is some science to back up these ideas it is simply what you think. Scientists think differently, and it due to actual scientific evidence. We could use the human sickle cell trait as an example. If you compare the map of the sickle cell trait with a map of endemic malaria the two overlap. This isn’t random.

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How does symbiosis cause traits to emerge?

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Beats me. Margulis took the secret to her grave, apparently.

As far as I know, Margulis was focused more on endosymbiosis as it related to the early evolution of eukaryotes and nucleated cells. These seem to be more one-off events than a pervasive mechanism through the whole of evolution.

This is not positive selection. The requirement is to correlate DNA changes to improvement in fitness or reproductive success.

In an environment with malaria the sickle cell trait does improve fitness. We even know the specific DNA changes involved.

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